just imagine that your main character can see into the water (because water is clear and not an opaque blue). A quick survey would tell him/her that there is no pokemon near where he/she is trying to fish and there is no point in keeping the rod hanging there.

This theory, however, doesn't explain why recasting the rod two seconds later will suddenly attract pokemon---3DS Friend Code: 5413-0006-7792PM me so I can add you as well!